6CD7

Crystal structure of APH(2")-IVa in complex with plazomicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Plazomicin Retains Antibiotic Activity against Most Aminoglycoside Modifying Enzymes.

Cox, G.Ejim, L.Stogios, P.J.Koteva, K.Bordeleau, E.Evdokimova, E.Sieron, A.O.Savchenko, A.Serio, A.W.Krause, K.M.Wright, G.D.

(2018) ACS Infect Dis 4: 980-987

  • DOI: 10.1021/acsinfecdis.8b00001
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plazomicin is a next-generation, semisynthetic aminoglycoside antibiotic currently under development for the treatment of infections due to multidrug-resistant Enterobacteriaceae. The compound was designed by chemical modification of the natural prod ...

    Plazomicin is a next-generation, semisynthetic aminoglycoside antibiotic currently under development for the treatment of infections due to multidrug-resistant Enterobacteriaceae. The compound was designed by chemical modification of the natural product sisomicin to provide protection from common aminoglycoside modifying enzymes that chemically alter these drugs via N-acetylation, O-adenylylation, or O-phosphorylation. In this study, plazomicin was profiled against a panel of isogenic strains of Escherichia coli individually expressing twenty-one aminoglycoside resistance enzymes. Plazomicin retained antibacterial activity against 15 of the 17 modifying enzyme-expressing strains tested. Expression of only two of the modifying enzymes, aac(2')-Ia and aph(2″)-IVa, decreased plazomicin potency. On the other hand, expression of 16S rRNA ribosomal methyltransferases results in a complete lack of plazomicin potency. In vitro enzymatic assessment confirmed that AAC(2')-Ia and APH(2'')-IVa (aminoglycoside acetyltransferase, AAC; aminoglycoside phosphotransferase, APH) were able to utilize plazomicin as a substrate. AAC(2')-Ia and APH(2'')-IVa are limited in their distribution to Providencia stuartii and Enterococci, respectively. These data demonstrate that plazomicin is not modified by a broad spectrum of common aminoglycoside modifying enzymes including those commonly found in Enterobacteriaceae. However, plazomicin is inactive in the presence of 16S rRNA ribosomal methyltransferases, which should be monitored in future surveillance programs.


    Organizational Affiliation

    Department of Microbiology, Immunology and Infectious Diseases, Health Research Innovation Centre , University of Calgary , 3330 Hospital Drive NW, HRIC-2C66 , Calgary , Alberta T2N 4N1 , Canada.,Achaogen , One Tower Place, Suite 300 , South San Francisco , California 94080 , United States.,Center for Structural Genomics of Infectious Diseases (CSGID) and Department of Chemical Engineering and Applied Chemistry , University of Toronto , Toronto , Ontario M5G 1L6 , Canada.,M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine , McMaster University , 1280 Main Street West , Hamilton , Ontario L8N 4K1 , Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APH(2'')-Id
A, B
302Enterococcus casseliflavusMutation(s): 0 
Gene Names: aph(2'')-Id
Find proteins for O68183 (Enterococcus casseliflavus)
Go to UniProtKB:  O68183
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDS
Query on EDS

Download SDF File 
Download CCD File 
B
(2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-4-{[(2S,3R)-3-amino-6-{[(2-hydroxyethyl)amino]methyl}-3,4-dihydro-2H-pyran-2-yl]oxy}-2-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-3-hydroxycyclohexyl]-2-hydroxybutanamide
plazomicin
C25 H48 N6 O10
IYDYFVUFSPQPPV-PEXOCOHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.455α = 90.00
b = 101.813β = 98.47
c = 72.921γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXmodel building
PHENIXrefinement
PHENIXphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History 

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection, Database references
  • Version 1.2: 2018-06-20
    Type: Data collection, Database references
  • Version 1.3: 2019-12-18
    Type: Author supporting evidence